SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave
Maria Bousali,
Aristea Dimadi,
Evangelia-Georgia Kostaki,
Sotirios Tsiodras,
Georgios K. Nikolopoulos,
Dionyssios N. Sgouras,
Gkikas Magiorkinis,
George Papatheodoridis,
Vasiliki Pogka,
Giota Lourida,
Aikaterini Argyraki,
Emmanouil Angelakis,
George Sourvinos,
Apostolos Beloukas,
Dimitrios Paraskevis,
Timokratis Karamitros
Affiliations
Maria Bousali
Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
Aristea Dimadi
Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
Evangelia-Georgia Kostaki
Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece
Sotirios Tsiodras
4th Department of Internal Medicine & Infectious Diseases, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece
Georgios K. Nikolopoulos
Medical School, University of Cyprus, 2029 Nicosia, Cyprus
Dionyssios N. Sgouras
Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
Gkikas Magiorkinis
Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece
George Papatheodoridis
Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, “Laiko” General Hospital of Athens, 11527 Athens, Greece
Vasiliki Pogka
Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. Results: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50–100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0–19 y.o. decreased only in those regions where schools’ closure was combined with a lockdown. Conclusions: The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing.
